Here's my position on it as I read and understand this (Like anyone cares, but here goes). But then, I'm a hardliner on quality work. (Not that I always do such myself, but I am solely accountable for my own mistakes).
The hull of the boat is paramount, kinda like the uni-body construction of a car. If I'da paid someone, or any of us had, to reupholster my car and they cut up parts of the floor and substructure of the vehicle, or drilled holes and ran bolts/screws threatening the integrity of the vehicle well outside the scope of the intended work, I'd be looking for more than just a simple fix. Now you have down time too, and honestly, Tony, you've been unknowingly running an unsafe boat for weeks now.
One of those screws could have caused a major crack or worse at speed. Not likely, but possible. This from a reputable shop?
I understand mistakes happen, they happen every day in my business, and I've even done quite a few on my own boats

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I can't tell you how many free appliances, tile jobs, carpet jobs or door installs we have eaten because of these mistakes and my propensity to make the customer happy. It may or may not be an everyday occurrance justifying trash talking the shop. Could just be a newbie or trainee mistake. My point is, you should, and deserve to be compensated for it, and they have now screwed up (Pardon the pun) an otherwise cherry hull! Whether they fix it or not, there should still be something off your original bill IMHO.
Ray